├── .gitignore ├── COPYRIGHT.txt ├── INSTALL.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── boolean2 ├── __init__.py ├── boolmodel.py ├── network.py ├── odict.py ├── plde │ ├── __init__.py │ ├── defs.py │ ├── helper.py │ └── model.py ├── ply │ ├── __init__.py │ ├── cpp.py │ ├── ctokens.py │ ├── lex.py │ ├── yacc.py │ └── ygen.py ├── ruleparser.py ├── state.py ├── timemodel.py ├── tokenizer.py └── util.py ├── docs └── manual.zip ├── examples ├── projects │ ├── LGL │ │ ├── LGL-plot.png │ │ ├── LGL-plot.py │ │ ├── LGL-simulation.py │ │ └── LGL.txt │ ├── README.txt │ ├── aba │ │ ├── ABA-plot.png │ │ ├── ABA.txt │ │ ├── Aba-plot.py │ │ └── Aba-simulation.py │ ├── demos │ │ ├── demo-override.py │ │ ├── demo-plde.py │ │ ├── demo-rules.txt │ │ └── demo-sync.py │ └── immune │ │ ├── Bb-compartmental.csv │ │ ├── Bb-concentration.csv │ │ ├── Bb-plot.png │ │ ├── Bb-plot.py │ │ ├── Bb-simulation.py │ │ ├── Bb.txt │ │ ├── localdefs.py │ │ └── overrides.py ├── samples │ ├── all-initial-states.py │ ├── extend-getvalue.py │ ├── extend-rules.py │ ├── extend-setvalue.py │ ├── singlepick.py │ ├── threenodes.py │ ├── timemodel.py │ └── timemodel.txt └── tutorials │ ├── t-01.py │ ├── t-02.py │ ├── t-03.py │ ├── t-04.py │ ├── t-05.py │ ├── t-06.py │ └── tutorial_explain.doc ├── makedist.sh ├── scripts ├── network_repair_functions.py ├── network_repair_tutorial.py └── sample_network.txt ├── setup.py └── tests ├── test-params.csv ├── test_all.py ├── test_codegen.py ├── test_engine.py ├── test_engine_noranks.py ├── test_helper.py ├── test_sync.py └── testbase.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ialbert/booleannet/HEAD/.gitignore -------------------------------------------------------------------------------- /COPYRIGHT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ialbert/booleannet/HEAD/COPYRIGHT.txt 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